Difference between revisions of "Evidence Code Ontology"

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** There are 40 obsolete ECO terms in the releases/2020-05-15
** There are 40 obsolete ECO terms in the releases/2020-05-15
= Example obo and ace entries =
*Running the script:
#In the /home/acedb/kimberly/citace_upload/ro/ontology2ace directory on tazendra, use the wget command and the above URL to download the ro.obo input file
#Greek characters used in some of the definitions for the RO terms (as an example, see id: BFO:0000063 name: precedes) need to be converted to text that ACeDB can render by doing the following (note that we tried to incorporate this as part of the script, but couldn't figure out a way to correctly recognize these characters programtically):
*In one terminal window, open the ro.obo file in a text editor
*In a second terminal window, open the convertGreekVim file in a text editor
*Globally replace the lower case alpha and omega symbols in ro.obo by copying and pasting the appropriate global replacement commands from convertGreekVim, e.g. :%s/α/alpha/g
**Sanity check:
***26 substitutions of lower-case alpha on 10 lines
***24 substitutions of lower-case omega on 9 lines
*Once the Greek characters have been replaced, run the parsing script and change the name of the output file from ro_terms.ace to ro_terms_WSnnn.ace

Revision as of 14:42, 1 June 2020


  • The Evidence and Conclusion Ontology will be incorporated into a future release of WormBase, aiming for WS278, and is proposed to eventually fully replace ?GO_code.

?ECO_term Model

 ?ECO_term Name UNIQUE ?Text
          Status UNIQUE Valid
          Alt_id ?Text
          Definition UNIQUE ?Text
          Synonym Broad ?Text
                  Exact ?Text
                  Narrow ?Text
                  Related ?Text
          Child ?ECO_term XREF Parent
          Parent ?ECO_term XREF Child
          Version UNIQUE Text

Other models affected for WS278

  • Will replace ?GO_code with ?ECO_term in:
    • ?GO_annotation
    • ?Phenotype
    • ?Disease_model_annotation (will eventually replace ?GO_code with ?ECO_term)
  • Will remove ?GO_code in:
    • ?Cell

Additional model cleanup? Are these tags being used at all?

  1. ?Gene - remove ?GO_term tag and associated info?
  2. ?Sequence - remove ?GO_term tag and associated info?
  3. ?CDS - remove ?GO_term tag and associated info?
  4. ?Transcript - remove ?GO_term tag and associated info?

Parsing Script for ?ECO_term Model

  • The parsing script to generate the eco_terms.ace file is on tazendra here:
    • /home/acedb/kimberly/citace_upload/eco/ontology2ace/eco_obo_to_eco_ace.pl
  • Output file:
    • eco_terms.ace
  • There are two types of entries in ro.obo
    • Term
    • Typedef
  • We'll only include the Term entries

ECO obo file to WB ace file mappings

ace field ECO field Action Example
ECO_term id: Add ECO id as is ECO:0000052
Name name: Add name as is (but see below) suppressor/enhancer interaction phenotypic evidence
Status is_obsolete: Populate with 'Valid' unless 'is_obsolete: true', then populate with Obsolete* Valid
Alt_id alt_id: Add alt_id as is ECO:0005018
Definition def: Remove quotation marks; add remaining text as is A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody. [ERO:0001362, url:http\://www.ncbi.nlm.nih.gov/books/NBK21589/\,http\://cores.ucsf.edu/protein-assay.html]
Synonym synonym Remove quotation marks; populate type from bracketed text; add remaining text as is Exact gain-of-function mutant phenotype evidence
Child n/a n/a n/a
Parent is_a: Add is_a parent id as is ECO:0000015
Version data-version: Add text following 'data-version:' releases/2020-05-15

  • Notes:
    • For names, may need to escape forward slashes
    • There are 40 obsolete ECO terms in the releases/2020-05-15

Example obo and ace entries